marker_getattr {pedtools}

Get marker attributes

Description

S3 methods retrieving marker attributes. They work on single marker objects and markers attached to ped objects (or lists of such).

Usage

genotype(x, ...)

## S3 method for class 'marker'
genotype(x, id, ...)

## S3 method for class 'ped'
genotype(x, markers = NULL, id, ...)

mutmod(x, ...)

## S3 method for class 'marker'
mutmod(x, ...)

## S3 method for class 'ped'
mutmod(x, marker, ...)

## S3 method for class 'list'
mutmod(x, marker, ...)

alleles(x, ...)

## S3 method for class 'marker'
alleles(x, ...)

## S3 method for class 'ped'
alleles(x, marker, ...)

## S3 method for class 'list'
alleles(x, marker, ...)

afreq(x, ...)

## S3 method for class 'marker'
afreq(x, ...)

## S3 method for class 'ped'
afreq(x, marker, ...)

## S3 method for class 'list'
afreq(x, marker, ...)

name(x, ...)

## S3 method for class 'marker'
name(x, ...)

## S3 method for class 'ped'
name(x, markers = NULL, ...)

## S3 method for class 'list'
name(x, markers = NULL, ...)

chrom(x, ...)

## S3 method for class 'marker'
chrom(x, ...)

## S3 method for class 'ped'
chrom(x, markers = NULL, ...)

## S3 method for class 'list'
chrom(x, markers = NULL, ...)

posMb(x, ...)

## S3 method for class 'marker'
posMb(x, ...)

## S3 method for class 'ped'
posMb(x, markers = NULL, ...)

Arguments

x

Either a marker object, a ped object or a list of ped objects.

...

Further arguments, not used.

id

The ID label of a single pedigree member.

marker, markers

The index or name of a marker (or a vector indicating several markers) attached to x.

Value

The associated marker attributes.

See Also

Setting marker attributes: marker_setattr and marker_inplace.

Examples

x = nuclearPed(1)
x = addMarker(x) # add empty marker

# Inspect default attributes
alleles(x, marker = 1)
afreq(x, marker = 1)
name(x, marker = 1)  # NA
chrom(x, marker = 1) # NA